The idea to allow one project to switch between Python 2 and Python 3 for individual files is more interesting, but practically speaking would lead to sort of a mess.
Yes, I believe key parts of the standard object model changed between the two (e.g. strings vs bytes, many of the magic methods and operators) making this nearly impossible. Every time objects would pass back and forth, they'd have to be converted, which is wasteful and bug-prone (and this is a whole mess of library code that the python3 guys probably did not want to write). You'd also need to load two different standard libraries, which would waste memory.
You only need to scan through the upgrade feature list to see how hard intercompatibility would have been. http://docs.python.org/3.0/whatsnew/3.0.html
Although I totally agree with Aaron that this would have allowed people to actually use Python 3 without fear, anything short of forcing the entire program and all of its modules to run in v3 mode as opposed to v2 mode would have been a disaster from a reliability and technical design standpoint. And that's closer to how things actually went down with 2to3, etc.